UNIX and Perl to the Rescue!: A Field Guide for the Life Sciences (and Other Data-rich Pursuits) New Edition

It's surely an introductory book, but much more is needed if you really want to do something with perl.

Book is treasure for a life science professional that is either learning or using Unix and Perl. The book has useful exercises that help with retaining and putting to use all the knowledge learned. I would recommend to not only life science professionals but to everyone.

This is a great tool for anyone who wants to learn UNIX and/or PERL, as the two sections are complementary yet independent of one another. The writing style is informal and accessible, and it does an effective job at walking the reader through some complex topics. This book is especially useful for those who are interested in learning how to parse through and manage large datasets created by next generation sequencing, and is a great first read (though more advanced users will likely need a more advanced text).

The title suggests a power tool, but the book is more like a primer. A very good primer!I used as a review of Perl and Unix commands and concepts. Some topics could be more deeply elaborated.

I am a biologist not a bioinformatician. Many advanced books are too difficult for me. Many prime books of computer languages are too unrelated to what I need. The book is very easy to understand. Besides, the minimum functions it introduce is enough for my analysis.

This is a great place to start with UNIX and Perl for anyone looking to apply computational techniques to biology. I've been programming for around 15 years now (Basic, C++, Java, Perl, and R), and this book is as good an introduction as any I've seen. It's also surprisingly comprehensive for it's brevity, including everything from, "This is a keyboard, and you won't be using your mouse. Here are the keys that you've never seen before (or have seen but never like this) `, =~, |, $, *, >>, %, etc.) all the way through your first "Hello World" program, to some very basic understandings of object-oriented programming, subroutines, libraries, packages, and relational databases. Many of these more advanced topics are only briefly covered, but they are here for those who want to wade into shark-infested waters.There are a few caveats, though.First, this book is not a quick read. Unless you're pretty skilled and intrepid, this is slow going, and it's going to involve a lot of trial and error. Be prepared to fall off of your horse quite a few times when you first start programming and using UNIX. (I'd also suggest that you create a dummy account on your computer until you're pretty familiar with UNIX, lest you accidentally wipe out everything that you've ever made on your computer...I've seen it happen, and it ain't pretty.) This is a consequence of the combination its breadth, depth, and brevity. You can expect to spend hours understanding some of the two to four page chapters, and truly mastering it could well take six months or more. That said, even dabbling in Perl can produce some spectacular results for biologists.Second, That said, there are those who are going to dislike this book, as it's focus is on programming rather than on biology. The background isn't biological, the problems don't lend themselves well to biology, and it takes making it to page 259 before biology really shows up (that's after you learn the basics both of the new operating system and the programming language, which can be pretty abstract and feel pretty distant from biology for a long, long time (especially due to how slow the average user will take to this dense text). If this sounds like you, and you want a book where the biological relevance is demonstrated in every example, I might suggest  Beginning Perl for Bioinformatics  instead. That book uses biological examples starting at chapter 1, but it isn't nearly as comprehensive a reference as this is.As nice as this book is, it isn't totally complete. To complement this (or to acquire a minimal bioinformatics programming library), there are a few things that I would suggest.First of all, the "camel book",  Perl in a Nutshell  is a good place to start. I've had copies of this floating around for a while, and it canI'd also recommend the "weasel book",  Regular Expressions Cookbook , as it makes the already powerful regular expressions that much more potent.Finally, I'd also suggest complementing your discovery of Perl with a discovery of R. This statistical tool/programming language is fantastic, robust, and will nicely complement the text-analysis tools available in Perl. Although I haven't read it, but this book  R in a Nutshell  looks to be a great place to start. R is a fantastic tool that I recommend to all research scientists, because making your graphs in Excel and Prism should get your papers summarily bounced from a respectable journal, along with a few laughs for your pains.If you decide to wade into these waters, these books are a great place to start. It can be daunting, but the payoff is usually worth it.Harkius

Perl is a flexible, powerful, and easy to program language. It has tremendous facilities for manipulating all sorts of data, doing I/O, creating web pages on the fly, and was once called "the duct tape that holds the web together." It has since been largely replaced by PHP and Javascript (and, to a lesser extent, by Ruby and other languages) for web programming, but it is still a tremendously useful tool for creating programs for manipulating data and for one-off data conversion projects. Perl code, being interpreted, isn't nearly as fast as compiled C code, but given the speed for today's computers, it's more than fast enough for most uses.While Windows and Macintosh computers have invaded laboratories and research institutions in large numbers in the last two or three decades, Unix- or increasingly, Linux- still reign supreme when it comes to shared processing and large-scale data gathering and data handling. The working researcher today, be they in the life sciences, the physical sciences, or the social sciences, typically has at their disposal some sort of shared Unix machine for data storage and handling. A great number of working scientists today have solid Unix and Perl skills, typically self-taught, picked up from a books and co-workers. There are a number of good texts available (particularly from O'Reilly) on Perl and Unix but this book attempts to present the essentials of both, without delving into details beyond those the typical researcher would need.The first 103 pages of this book are devoted to Unix- mostly working with files and directories.. It delivers a good overview of how the filesystem works, how $PATH variables work, and the bare essentials of file permissions, but surprisingly little about editing files, searching directories, and other topics I consider essential for using Unix. There's nothing at all on the find command- one of the most powerful and useful unix commands when it comes to handling data. The only editor mentioned in nano, which is not found in every system, and there's only three pages on nano. I would have liked to see a few pages on vi, which is universal and capable of very powerful data manipulation with simple commands. There's a brief later chapter entitled "Advanced Unix" that does get in to the uses of cat, ps and grep, but it's only four pages long. I was pleased to see a reference to CPAN, an invaluable tool for the programmer, but it contains a use of "sudo" without getting in the power (and danger!) of sudo, and sudo doesn't even show up in the index. As a Unix manual, I'd have to give this book only three stars.The perl section is much better, and takes up about two thirds of the text. There's a fair amount on good programming practice, like emphasizing the use of 'strict' early on. REGEXP is covered, briefly, but in enough detail that the reader could construct some simple matches. Hashes are dealt with in a clear manner, and there are clear examples given for every topic- although the examples tend to be brief. Like a number of other reviewers, I would have liked to see some specific examples drawn from the life sciences, as the book promises. Perhaps a search for certain codons in a DNA string, or some simple time-series searches, or data smoothing.This is a good enough intro to using unix perl, but I think a working researcher would profit greatly by also reading, at a minimum, Tom Christian's Perl Cookbook, which is chock full of chunks of usable code for doing things like searching, I/O, and so forth. Randall Schwartz's Learning Perl, Fourth Edition would be a better place for the Perl beginner, and Learning the UNIX Operating System, Fifth Edition would be a better introduction and working manual for the novice Unix user.

This is a great help for anyone needing to use Unix for biosciences. I've just been told I need it for my internship so I got this book to help me learn. Within 3 days I've gone through the basic Unix section and can find my way around and deal with text files. I don't think I'd have picked it up quite this quickly without the help this book provides. It's not like other (boring) coding books which just give you a list of commands and examples, there's extra comments that have actually made me laugh while learning it! Overall it's a great book and I'd really recommend it for anyone trying to learn Unix

It does exactly what it says on the tin! My son is certainly happy with it. Well worth the money.

El libro es muy bueno y fácil de seguir, es sencillo y se adapta a un lector que no tiene experiencia con terminal de linea de comando. En menos de una semana ya me siento cómodo trabajando con cosas básicas en linea de comando tanto de Mac OS X como en diversas distros de Linux.Quizá lo único que se podría reprochar es que a pesar que se dice orientado hacia ciencias de la vida, en realidad la enorme mayoría del tiempo tiene un abordaje mas general. (al menos hasta donde he leído que es los capitulos introductorios y la primer parte de UNIX).Totalmente recomendado.

Writers did a good job in making this book a interesting read!I love their writing style and the flow in the book.Highly recommended.